-- Convenience routine for creating alleles from strings of bases
-- Convenience constructor for VCFFilterHeader line whose description is the same as name
-- VariantContextTestProvider creates all sorts of types of VariantContexts for testing purposes. Can be reused throughtout code for BCF, VCF, etc.
-- Created basic BCF2WriterCodec tests that consumes VariantContextTestProvider contexts, writes them to disk with BCF2 writer, and checks that they come back equals to the original VariantContexts. Actually worked for some complex tests in the first go
-- Added VCFHeader() constructor that makes an empty header, and updated VariantRecalibrator to use it
-- Update build.xml to build vcf.jar with updated paths and bcf2 support.
-- Moved VCF and BCF writers to variantcontext.writers
-- Updated vcf.jar build path
-- Refactored VCFWriter and other code. Now the best (and soon to be only) way to create these files is through a factory method called VariantContextWriterFactory. Renamed the general VCFWriter interface to VariantContextWriter which is implemented by VCFWriter and BCF2Writer.
-- Refactored VCF writers into vcf.writers package
-- Moved BCF2Writer to bcf2.writer
-- Updates to all of the walkers using VCFWriter to reflect new packages
-- A large number of files had their headers cleaned up because of this as well
-- Restructured code to separate the MISSING value in java (currently everywhere a null) from the byte representation on disk (an int).
-- Now handles correctly MISSING qual fields
-- Refactored setting of contigs from VCFWriterStub to VCFUtils. Necessary for proper BCF working
-- Added VCFContigHeaderLine that manages the order for sorting, so we now emit contigs in the proper order.
-- Cleaned up VCFHeader operations
-- BCF now uses the right header files correctly when encoding / decoding contigs
-- Clean up unused tools
-- Refactored header parsing routines to make them more accessible
-- More minor header changes from Intellij
This bug will happen in all adapter/wrapper classes that are passed a resource, and then in their close method they ignore requests to close the wrapped resource, causing a leak when the adapter is the only one left with a reference to the resource.
Ex:
public Wrapper getNewWrapper(File path) {
FileStream myStream = new FileStream(path); // This stream must be eventually closed.
return new Wrapper(myStream);
}
public void close(Wrapper wrapper) {
wrapper.close(); // If wrapper.close() does nothing, NO ONE else has a reference to close myStream.
}
* For some reason, the original implementor decided to use Booleans instead of booleans and didn't always check for null so we'd occasionally get a NPE. Switched over to booleans.
* We'd also generate a NPE if SAMRecord writing specific arguments (e.g. --simplifyBAM) were used while writing to sdout.
The practical differences between version 1.0 and this one (v1.1) are:
* the underlying data structure now uses arrays instead of hashes, which should drastically reduce the memory overhead required to create large tables.
* no more primary keys; you can still create arbitrary IDs to index into rows, but there is no special cased primary key column in the table.
* no more dangerous/ugly table operations supported except to increment a cell's value (if an int) or to concatenate 2 tables.
Integration tests change because table headers are different.
Old classes are still lying around. Will clean those up in a subsequent commit.
Mark DePristo
Guillermo del Angel
Ryan Poplin
Eric Banks
Khalid Shakir